Structure #142560

Summary

Genome/Assembly	hg17
Chromosome/Contig	chr4
Strand	-
Position	173,327,586 - 173,327,680
Number of sequences	5
Organisms	human, dog, mouse, rat, chicken
Mean pairwise identity	70.38
Columns	108
Mean single MFE	-28.78
Consensus MFE	-20.68
Combinations/base pair	34 / 24 = 1.42
SCI	0.72
z-score	-4.17
RNA class probability	0.999539

This structure is part of cluster 78719

Alignment

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RNAz output

	  
###########################  RNAz 0.1.1  #############################

 Sequences: 5
 Slice: 1 to 108
 Columns: 108
 Strand: +
 Mean pairwise identity:  70.38
 Mean single sequence MFE: -28.78
 Consensus MFE: -20.68
 Energy contribution: -22.56
 Covariance contribution:   1.88
 Mean z-score:  -4.17
 Structure conservation index:   0.72
 SVM decision value:   3.70
 SVM RNA-class probability: 0.999539
 Prediction: RNA

######################################################################

>hg17.chr4/173327680-173327586
AAUUAAGAUUUCAACUUGCUUGAACAGAAUCUCAUUUCCUUGAAAUACAGCAGGAGCAGUAUUUCAAGGAAAUGAGAUUCAUCUUCACACUGAG
....((((((((((.....)))))..((((((((((((((((((((((.((....)).)))))))))))))))))))))))))))......... ( -38.70)
>canFam1.chr25/25774222-25774128
AAUUAAGAUUUCAACUUGCUUGAACAGAAUCUCAUUUCCUUGAAAUACAGUAGAAGCAGUAUUUCAAGGAAAUGAUAUUCAUCUUCACACUGAG
....((((((((((.....)))))..((((.(((((((((((((((((.((....)).))))))))))))))))).)))))))))......... ( -30.60)
>mm5.chr8/0-94
AAUUAAAAUUUCUACUUGCUUUAGCAGUAUCUCAUUUCCUUGAGAUGAAGCAGGAGUGAUGCUUCAAGGAAAUGAGAUUCAUCUUCAUACAGAG
..........(((...(((....)))(.(((((((((((((((.....((((.......))))))))))))))))))).)..........))). ( -27.80)
>rn3.chr16/34798804-34798715
AAUAUUUCUACUUGCUUUAACAGAAUCCCAUUUCCUUGGGAUGAAGUGAAGUGAUUCUUCAAGGAAAUGAGAUUCAUUUUCAUACAGAG
......(((..(..(((((.....((((((......))))))....)))))..)........(((((((.....)))))))....))). ( -22.30)
>galGal2.chr4/43456058-43455950
AAUAAAGAUUUCAAGCUGUUAAGGGGCAGAGGGGAGAAAAAGAUCUGCUCUCCUUGUAAUAUCUCACUAGCAGCAUUCCAGAGAAACAGGCUUCCAUUUCAUGCUGAG
..............(((((((..(((..((((((((...........)))))))).......)))..)))))))....(((.((((..((...)).))))...))).. ( -24.50)
>consensus
AAUUAAGAUUUCAACUUGCUU______________GAACAGAAUCUCAUUUCCUUGAAAUAAAGCAGAAGCAGUAUUUCAAGGAAAUGAGAUUCAUCUUCAUACUGAG
........................................((((((((((((((((((((((.((....)).)))))))))))))))))))))).............. (-20.68 = -22.56 +   1.88)

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Consensus structure

Secondary structure graph

Secondary structure

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Montain plot

Secondary structure

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Dotplot

Secondary structure

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